Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

glut fatal error in tkmedit.bin visual with necessary capabilities not found
by Alex Liu 16 Mar '12

16 Mar '12

Hello all, I'm relatively new to freesurfer so this may be a simple fix. I was using freesurfer the other day and I came across the following message: GLUT: fatal error in tkmedit.bin visual with necessary capabilities not found. I'm using a mac laptop and I'm not sure if this is just an issue with computer settings. Any info on this matter would be greatly appreciated. Thank you. -- Alex

1 0

License Installation problem
by Talvadkar, Kunal Girish 15 Mar '12

15 Mar '12

Hi, I tried installing the free surfer license,but was not able to do so,if anyone could help me with a detailed approach to this,I would be most grateful.I am saying detailed cause i am not familiar with some computing procedures. Thanks, Kunal

2 1

Re: [Freesurfer] strangely low lhCorticalWhiteMatterVol estimate
by Michael Harms 15 Mar '12

15 Mar '12

Hi Doug, As a post-mortem to this thread, in the process of going to "tweak" the wm.mgz as you suggested, I noticed that there were actually some substantial errors in the surfaces in the calcarine, presumably due to topology correction gone astray. So, whether or not that precipitated the problem with the filling operation of mris_wm_volume, it was something that needed wm editing, and once that was done, the ensuing lhCorticalWhiteMatterVol was again normal. cheers, -MH > On Thu, 2012-03-01 at 13:29 -0500, Douglas N Greve wrote: > It must be that the shell is not quite getting closed. Didn't Gheorghe > use a ray tracing algorithm for this? > > Bruce Fischl wrote: > > hmmmmm, I don't understand why the filling is failing then. I can't > > remember who's code this is. I think it started life as Andre's > > (shocking!), but maybe Krish or Martin has taken it over since then? > > > > On Thu, 1 Mar 2012, Douglas N Greve wrote: > > > >> > >> mris_euler_number surf/lh.white > >> euler # = v-e+f = 2g-2: 166103 - 498303 + 332202 = 2 --> 0 holes > >> F =2V-4: 332202 = 332206-4 (0) > >> 2E=3F: 996606 = 996606 (0) > >> total defect index = 0 > >> > >> mris_euler_number surf/rh.white > >> euler # = v-e+f = 2g-2: 167114 - 501336 + 334224 = 2 --> 0 holes > >> F =2V-4: 334224 = 334228-4 (0) > >> 2E=3F: 1002672 = 1002672 (0) > >> total defect index = 0 > >> > >> > >> Bruce Fischl wrote: > >>> what is the euler number for the white surface for this subject > >>> (mris_euler_number)? > >>> On Thu, 1 Mar 2012, Douglas N Greve wrote: > >>> > >>>> Hi Mike, I *think* I've found the problem with this subject. The way > >>>> that the volume inside the white surface is computed is to create a > >>>> high-res volume (.25mm iso), then create a shell based on the > >>>> intersection of the faces with the volume. The outside of the shell is > >>>> "flooded", the result is inverted to give a map of voxels inside the > >>>> white surface. This includes subcortical voxels, so the voxels > >>>> known to > >>>> be in the WM from the aseg are added. The .25mm voxels that are > >>>> labeled > >>>> as cortical gray matter are also included since these represent > >>>> partial > >>>> volume that are really WM. So far so good. I think the problem is that > >>>> the shell for this subject has a hole in it, so the flood leaks into > >>>> most the interior. When inverted, there are very few voxels left > >>>> and so > >>>> the WM volume is way too low. It might take a while to find a solution > >>>> to this, so I just wanted to give you a heads up. One possible > >>>> work-around is to make an edit that causes the surface to change. > >>>> It is > >>>> probably the case that even a small change causes the hole to fill and > >>>> everything works out. > >>>> > >>>> doug > >>>> > >>>> Michael Harms wrote: > >>>>> Hello, > >>>>> > >>>>> Anyone have a chance to look at this? Should we just forget about > >>>>> trying to get an accurate lhCorticalWhiteMatterVol value for this > >>>>> subject? > >>>>> > >>>>> thanks, > >>>>> -MH > >>>>> > >>>>> On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote: > >>>>> > >>>>>> Hi guys, > >>>>>> > >>>>>> We have a subject processed with FS v5.1 in which > >>>>>> lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781 > >>>>>> mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume > >>>>>> lh.white' > >>>>>> returns 287261 and running mri_segstats without the --excl-ctxgmwm > >>>>>> option returns a Left-Cerebral-White-Matter volume of 245169. > >>>>>> 'mris_euler_number' indicates no problems with lh.white. > >>>>>> > >>>>>> Running 'mris_wm_volume' on its own generates the same value of > >>>>>> 33781. > >>>>>> I also tried running 'mris_wm_volume' with the -v option to see > >>>>>> if any > >>>>>> interesting messages popped up, but got the message "unknown > >>>>>> option -v". > >>>>>> > >>>>>> Any idea what is going wrong here? So you can see for yourself, > >>>>>> I went > >>>>>> ahead and uploaded the subject's processed data to your FTP server > >>>>>> (110107_L206.tgz) > >>>>>> > >>>>>> thanks, > >>>>>> -MH > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>> > >>> > >> > >> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. >

1 0

Q: Tkmedit
by Yiyu Chou 15 Mar '12

15 Mar '12

Dear FS users,

2 1

HELP needed to improving quality while processing CHILDREN'S DATA
by Karla Zúñiga 15 Mar '12

15 Mar '12

Hello Freesurfers, I am new using freesurfer and I would like to know if any of you have some ideas (tools, tips, ...) on how to improve the quality of my results while processing structural T1 data from children aged 5 to 7 years old. Syncerly, Karla -- Karla Monzalvo Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Tél : 33 (0)1 69 08 90 66 Fax : 33 (0)1 69 08 79 73 karla.monzalvo(a)cea.fr http://www.unicog.org/

2 1

Crippled fiber tracts in healthy subjects (TRACULA)
by Ansgar Furst 15 Mar '12

15 Mar '12

Hi, We are using the ADNI Acc 3D FSPGR for structurals and 30 directional (5 B0s) repeat sequence for DTI which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely crippled tracts which, however, is not consistent with the FA maps. using

2 1

export hippocampal subfields using mri_binarize
by Catarina Duarte 15 Mar '12

15 Mar '12

Hi all, I am trying to export the hippocampal subfields generated in Freesurfer 5.1. To do that I use mri_binarize with a minimum voxel threshold of 150 and a maximum of 255. However, some of these regions appear overlapped. Why does this happen if a minimum threshold of 150 correponds to a probability higher than 50%? Thank you in advance. Best, Catarina Duarte

2 1

Q: Tkmedit
by Yiyu Chou 15 Mar '12

15 Mar '12

Dear FS users, Please have a look at the attached fig: As shown on the left (using Tkmedit), you will see some "straight lines", but they were not shown if using other software package (ex: mipav - on the right). Do you know what might be wrong on tkmedit ? Thanks in advance !! Regards, Yi-Yu

2 1

WG: Save segmentation results as nifi files
by Fellhauer, Iven 15 Mar '12

15 Mar '12

________________________________________ Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi files Dear all, in which space are the output files stored? If they are not stored in MNI space, which steps are necessary to convert these images into MNI space. Best regards, Iven Fellhauer ________________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Dienstag, 31. Januar 2012 18:33 Bis: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] WG: Save segmentation results as nifi files There's not a separate GM, WM, and CSF. You can create these from the segmentations with mri_binarize. In general, it is run something like this: mri_binarize --i aparc+aseg.mgz --match id1 id2 --o output.nii where id1 and id2 are structure codes from $FREESURFER_HOME/FreeSurferColorLUT.txt For all WM use: 2, 41, 77, 7, 46, 251-255 For all ventricular CSF and choroid plexus use: 4, 5, 14, 45, 44, 72, 31, 63, 15 For GM, use all the above plus 0, then add the --inv option to invert the mask (basically creating a mask of everything that is not GM and inverting it). doug Fellhauer, Iven wrote: > Hi Bruce > > And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur? > > Best regards, > > Iven > > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Gesendet: Montag, 30. Januar 2012 15:20 > An: Fellhauer, Iven > Cc: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Save segmentation results as nifi files > > Hi Ivan > > you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so: > > mri_convert aseg.mgz aseg.nii.gz > > or > > mri_convert aseg.mgz aseg.nii > > should do the trick > > cheers > Bruce > > > > On Mon, > 30 Jan 2012, Fellhauer, Iven wrote: > > >> Dear all, >> >> >> >> I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I >> want to store the segmentation results in a spm like way. One nifti >> file for each matter. Can I do this with freesurfer? And how can I do >> this with freesurfer? >> >> >> >> Best regards, >> >> >> >> Iven Fellhauer >> >> >> >> ---------------------------------------------------------------- >> >> Universitätsklinikum Heidelberg >> >> Zentrum für Psychosoziale Medizin >> >> Klinik für Allgemeine Psychiatrie >> >> Sektion für Gerontopsychiatrie >> >> Voßstr. 4 >> >> 69115 Heidelberg >> >> Tel.: +49 (0) 6221 - 56 7578 >> >> Email: iven.fellhauer(a)med.uni-heidelberg.de >> >> >> >> >> >> > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 1

Cluster-Size in Qdec
by Dusan Hirjak 14 Mar '12

14 Mar '12

Dear Freesurfer experts, I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan

2 4

← Newer
1
...
9
10
11
12
13
14
15
...
21
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer March 2012